System 1 - Refinery system
None of the three systems have a good setup for rocky planets, so the best I could come up with is a RMC with no volcanism, yes bio signals, 5 ground slots and 2 space slots (1 being taken up by a commercial port as the initial port). Next to it is an RMC with no volcanism, no bio signals, 3 ground slots and 0 space slots. The initial idea was to build a surface out post on the first one (for population and composites), along with 4 refinery hubs for strong links, and a Coriolis in orbit. On the 2nd planet 3 refinery hubs for weak links. The rest of the space slots in the system were going to be farms (to boost standard of living) and relay / security installations (to boost security).
+0.15 refinery economy from 3 weak links is unlikely to be worth having. If you make one of them another T1 surface port you'll get a lot more refined goods that way.
1. Are those bio signals on the first planet going to mess up my refinery production? I know agriculture isn't supposed to mess up refinery much, but I don't know how much 'much' is.
The only refinery product which Agriculture consumes is Biowaste, which is easy enough to get from other sources.
However the bio signals will also add the Terraforming economy, which consumes Polymers, Semiconductors, Superconductors, Gold and Silver. If you do build a T1 surface port on the other planet as well that will give you somewhere which can produce those.
2. Same question about the space farms
Those are safer, since they just produce Agricultural influence.
3. I know the military generated by the security stations is a no no for refinery economies because they eat CMMs, but how else am i supposed to boost security?
Two main options here.
Option 1: security buildings which don't generate military weak links
1) A Military T1 outpost gives +2 security and provided it's the only port orbiting that planet won't generate a weak link. So you can put one each of those around spare planets.
2) A Government installation gives +2 security as well as other boosts, is cheaper to build, has no economy type at all ... but does use T2 points you'll probably want to save for the hubs.
In this case because building up security is fairly slow, unless you have a lot of spare slots don't expect to get to high security - just balancing out the other things you're building to stay above zero will be a lot of work
Option 2: put an Anarchy faction in charge of the system, so that most of the effects of the Security variable become irrelevant.
System 2 - Industrial system
This one has three ice planets: #1 no volcanism, yes bio, 5 ground slots, 2 space slots. #2 no volcanism, no bio, 3 ground slots, 2 space slots. #3 no volcanism, no bio, 3 ground slots, 1 space slots. Original plan was to build a planetary outpost on #1 withe industrial hubs for strong links, Coriolis in orbit, and industrial hubs on #2 and #3 for week links.
1. I was planning to build a outpost in the refinery system for the materials that needed to be produced on the surface, but I don't have that issue with industrial. Is it still good to have for the population? Or should I replace it with another hub?
Planetary outposts give a lot of population which means a lot of production.
Again, weak links are pretty worthless for adding production - you get +0.05 per link, whereas another surface port in the same slot would give you +1 or more.
Another thought: rather than industrial hubs, consider industrial settlements - they're cheaper to build, the T2 gives the same strong links as a hub, there's a T1 variant to get you T2 points, they don't damage standard of living at all, and they have a really good boost to development level which is a major contributor to market sizes. Also you'll get a more interesting choice of missions involving them later.
2. Not sure how bio signals affect industrial?
Both Agriculture and Terraforming consume industrial products. Avoid for the planet with the Coriolis.
You can build a T1 surface outpost with Industrial as its baseline economy - that completely ignores the planet type, so you can put that on the bio-signal world and be fine.
3. Also no sure what the economies to avoid for industrial systems, so not sure how the farms and security stations will affect these.
Every other economy consumes industrial products, and most economies consume most industrial products. Try to avoid weak links of any other type. Government installations give enough standard-of-living boost that you probably don't need the farms, though - since Industrial, unlike Refinery, won't be reducing standard of living in the first place.
System 3 - Extraction / High Tech / Tourism
This is my 'for fun' system that wanted to raise the tech as high as possible and have some tourist spots. There's a lot of rings and belts so i thought about extraction for the wealth.
1. Is something in the Extraction / High Tech / Tourism combo going to cannibalize the other economies?
2. Same questions about the farms and security stations.
Yes, this system is going to be a complete mess for economic production and consumption, so don't worry about it. You'll get most but not all minerals for export out of the Extraction stations (since most but not all of them are only consumed by Refinery) and you'll get a few of the high-tech goods which are only needed by Refinery/Industrial, but everything else will be down to luck and the details of exactly what you build.
Mostly that's fine as you weren't planning to use it for trade in the first place - but you can get some uninterrupted high-tech output to help with local colonisation supplies by picking any planet with at least two slots, and building two HT surface T1 outposts on it (using the type which comes with its own high-tech economy, which is also another +5 tech level each time) - one of the outposts will shield the other from weak links, giving you a single-type HT economy with high production levels and a large landing pad.